Merge branch 'master' into torfjelde/step-warmup

Author: torfjelde

Project.toml

@@ -3,12 +3,13 @@ uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 keywords = ["markov chain monte carlo", "probablistic programming"]
 license = "MIT"
 desc = "A lightweight interface for common MCMC methods."
-version = "4.5.0"
+version = "5.0.0"
 
 [deps]
 BangBang = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
 ConsoleProgressMonitor = "88cd18e8-d9cc-4ea6-8889-5259c0d15c8b"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
@@ -21,6 +22,7 @@ Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
 [compat]
 BangBang = "0.3.19"
 ConsoleProgressMonitor = "0.1"
+FillArrays = "1"
 LogDensityProblems = "2"
 LoggingExtras = "0.4, 0.5, 1"
 ProgressLogging = "0.1"

docs/src/api.md

@@ -79,14 +79,16 @@ Common keyword arguments for regular and parallel sampling are:
 - `discard_initial` (default: `num_warmup`): number of initial samples that are discarded. Note that
   if `discard_initial < num_warmup`, warm-up samples will also be included in the resulting samples.
 - `thinning` (default: `1`): factor by which to thin samples.
+- `initial_state` (default: `nothing`): if `initial_state !== nothing`, the first call to [`AbstractMCMC.step`](@ref)
+  is passed `initial_state` as the `state` argument.
 
 !!! info
     The common keyword arguments `progress`, `chain_type`, and `callback` are not supported by the iterator [`AbstractMCMC.steps`](@ref) and the transducer [`AbstractMCMC.Sample`](@ref).
 
 There is no "official" way for providing initial parameter values yet.
-However, multiple packages such as [EllipticalSliceSampling.jl](https://github.com/TuringLang/EllipticalSliceSampling.jl) and [AdvancedMH.jl](https://github.com/TuringLang/AdvancedMH.jl) support an `init_params` keyword argument for setting the initial values when sampling a single chain.
-To ensure that sampling multiple chains "just works" when sampling of a single chain is implemented, [we decided to support `init_params` in the default implementations of the ensemble methods](https://github.com/TuringLang/AbstractMCMC.jl/pull/94):
-- `init_params` (default: `nothing`): if `init_params isa AbstractArray`, then the `i`th element of `init_params` is used as initial parameters of the `i`th chain. If one wants to use the same initial parameters `x` for every chain, one can specify e.g. `init_params = FillArrays.Fill(x, N)`.
+However, multiple packages such as [EllipticalSliceSampling.jl](https://github.com/TuringLang/EllipticalSliceSampling.jl) and [AdvancedMH.jl](https://github.com/TuringLang/AdvancedMH.jl) support an `initial_params` keyword argument for setting the initial values when sampling a single chain.
+To ensure that sampling multiple chains "just works" when sampling of a single chain is implemented, [we decided to support `initial_params` in the default implementations of the ensemble methods](https://github.com/TuringLang/AbstractMCMC.jl/pull/94):
+- `initial_params` (default: `nothing`): if `initial_params isa AbstractArray`, then the `i`th element of `initial_params` is used as initial parameters of the `i`th chain. If one wants to use the same initial parameters `x` for every chain, one can specify e.g. `initial_params = FillArrays.Fill(x, N)`.
 
 Progress logging can be enabled and disabled globally with `AbstractMCMC.setprogress!(progress)`.
 

src/AbstractMCMC.jl

@@ -8,6 +8,7 @@ using ProgressLogging: ProgressLogging
 using StatsBase: StatsBase
 using TerminalLoggers: TerminalLoggers
 using Transducers: Transducers
+using FillArrays: FillArrays
 
 using Distributed: Distributed
 using Logging: Logging

src/sample.jl

@@ -113,6 +113,7 @@ function mcmcsample(
     discard_initial::Int=num_warmup,
     thinning=1,
     chain_type::Type=Any,
+    initial_state=nothing,
     kwargs...,
 )
     # Check the number of requested samples.
@@ -145,9 +146,17 @@ function mcmcsample(
 
         # Obtain the initial sample and state.
         sample, state = if num_warmup > 0
-            step_warmup(rng, model, sampler; kwargs...)
+            if initial_state === nothing
+                step_warmup(rng, model, sampler; kwargs...)
+            else
+                step_warmup(rng, model, sampler, initial_state; kwargs...)
+            end
         else
-            step(rng, model, sampler; kwargs...)
+            if initial_state === nothing
+                step(rng, model, sampler; kwargs...)
+            else
+                step(rng, model, sampler, initial_state; kwargs...)
+            end
         end
 
         # Update the progress bar.
@@ -253,6 +262,7 @@ function mcmcsample(
     num_warmup=0,
     discard_initial=num_warmup,
     thinning=1,
+    initial_state=nothing,
     kwargs...,
 )
     # Determine how many samples to drop from `num_warmup` and the
@@ -267,9 +277,17 @@ function mcmcsample(
     @ifwithprogresslogger progress name = progressname begin
         # Obtain the initial sample and state.
         sample, state = if num_warmup > 0
-            step_warmup(rng, model, sampler; kwargs...)
+            if initial_state === nothing
+                step_warmup(rng, model, sampler; kwargs...)
+            else
+                step_warmup(rng, model, sampler, initial_state; kwargs...)
+            end
         else
-            step(rng, model, sampler; kwargs...)
+            if initial_state === nothing
+                step(rng, model, sampler; kwargs...)
+            else
+                step(rng, model, sampler, initial_state; kwargs...)
+            end
         end
 
         # Discard initial samples.
@@ -349,7 +367,8 @@ function mcmcsample(
     nchains::Integer;
     progress=PROGRESS[],
     progressname="Sampling ($(min(nchains, Threads.nthreads())) threads)",
-    init_params=nothing,
+    initial_params=nothing,
+    initial_state=nothing,
     kwargs...,
 )
     # Check if actually multiple threads are used.
@@ -373,8 +392,9 @@ function mcmcsample(
     # Create a seed for each chain using the provided random number generator.
     seeds = rand(rng, UInt, nchains)
 
-    # Ensure that initial parameters are `nothing` or of the correct length
-    check_initial_params(init_params, nchains)
+    # Ensure that initial parameters and states are `nothing` or of the correct length
+    check_initial_params(initial_params, nchains)
+    check_initial_state(initial_state, nchains)
 
     # Set up a chains vector.
     chains = Vector{Any}(undef, nchains)
@@ -425,10 +445,15 @@ function mcmcsample(
                                 _sampler,
                                 N;
                                 progress=false,
-                                init_params=if init_params === nothing
+                                initial_params=if initial_params === nothing
                                     nothing
                                 else
-                                    init_params[chainidx]
+                                    initial_params[chainidx]
+                                end,
+                                initial_state=if initial_state === nothing
+                                    nothing
+                                else
+                                    initial_state[chainidx]
                                 end,
                                 kwargs...,
                             )
@@ -458,7 +483,8 @@ function mcmcsample(
     nchains::Integer;
     progress=PROGRESS[],
     progressname="Sampling ($(Distributed.nworkers()) processes)",
-    init_params=nothing,
+    initial_params=nothing,
+    initial_state=nothing,
     kwargs...,
 )
     # Check if actually multiple processes are used.
@@ -471,8 +497,14 @@ function mcmcsample(
         @warn "Number of chains ($nchains) is greater than number of samples per chain ($N)"
     end
 
-    # Ensure that initial parameters are `nothing` or of the correct length
-    check_initial_params(init_params, nchains)
+    # Ensure that initial parameters and states are `nothing` or of the correct length
+    check_initial_params(initial_params, nchains)
+    check_initial_state(initial_state, nchains)
+
+    _initial_params =
+        initial_params === nothing ? FillArrays.Fill(nothing, nchains) : initial_params
+    _initial_state =
+        initial_state === nothing ? FillArrays.Fill(nothing, nchains) : initial_state
 
     # Create a seed for each chain using the provided random number generator.
     seeds = rand(rng, UInt, nchains)
@@ -509,7 +541,7 @@ function mcmcsample(
 
             Distributed.@async begin
                 try
-                    function sample_chain(seed, init_params=nothing)
+                    function sample_chain(seed, initial_params, initial_state)
                         # Seed a new random number generator with the pre-made seed.
                         Random.seed!(rng, seed)
 
@@ -520,7 +552,8 @@ function mcmcsample(
                             sampler,
                             N;
                             progress=false,
-                            init_params=init_params,
+                            initial_params=initial_params,
+                            initial_state=initial_state,
                             kwargs...,
                         )
 
@@ -530,11 +563,9 @@ function mcmcsample(
                         # Return the new chain.
                         return chain
                     end
-                    chains = if init_params === nothing
-                        Distributed.pmap(sample_chain, pool, seeds)
-                    else
-                        Distributed.pmap(sample_chain, pool, seeds, init_params)
-                    end
+                    chains = Distributed.pmap(
+                        sample_chain, pool, seeds, _initial_params, _initial_state
+                    )
                 finally
                     # Stop updating the progress bar.
                     progress && put!(channel, false)
@@ -555,22 +586,29 @@ function mcmcsample(
     N::Integer,
     nchains::Integer;
     progressname="Sampling",
-    init_params=nothing,
+    initial_params=nothing,
+    initial_state=nothing,
     kwargs...,
 )
     # Check if the number of chains is larger than the number of samples
     if nchains > N
         @warn "Number of chains ($nchains) is greater than number of samples per chain ($N)"
     end
 
-    # Ensure that initial parameters are `nothing` or of the correct length
-    check_initial_params(init_params, nchains)
+    # Ensure that initial parameters and states are `nothing` or of the correct length
+    check_initial_params(initial_params, nchains)
+    check_initial_state(initial_state, nchains)
+
+    _initial_params =
+        initial_params === nothing ? FillArrays.Fill(nothing, nchains) : initial_params
+    _initial_state =
+        initial_state === nothing ? FillArrays.Fill(nothing, nchains) : initial_state
 
     # Create a seed for each chain using the provided random number generator.
     seeds = rand(rng, UInt, nchains)
 
     # Sample the chains.
-    function sample_chain(i, seed, init_params=nothing)
+    function sample_chain(i, seed, initial_params, initial_state)
         # Seed a new random number generator with the pre-made seed.
         Random.seed!(rng, seed)
 
@@ -581,16 +619,13 @@ function mcmcsample(
             sampler,
             N;
             progressname=string(progressname, " (Chain ", i, " of ", nchains, ")"),
-            init_params=init_params,
+            initial_params=initial_params,
+            initial_state=initial_state,
             kwargs...,
         )
     end
 
-    chains = if init_params === nothing
-        map(sample_chain, 1:nchains, seeds)
-    else
-        map(sample_chain, 1:nchains, seeds, init_params)
-    end
+    chains = map(sample_chain, 1:nchains, seeds, _initial_params, _initial_state)
 
     # Concatenate the chains together.
     return chainsstack(tighten_eltype(chains))
@@ -604,7 +639,6 @@ tighten_eltype(x::Vector{Any}) = map(identity, x)
         "initial parameters must be specified as a vector of length equal to the number of chains or `nothing`",
     ),
 )
-
 check_initial_params(::Nothing, n) = nothing
 function check_initial_params(x::AbstractArray, n)
     if length(x) != n
@@ -617,3 +651,21 @@ function check_initial_params(x::AbstractArray, n)
 
     return nothing
 end
+
+@nospecialize check_initial_state(x, n) = throw(
+    ArgumentError(
+        "initial states must be specified as a vector of length equal to the number of chains or `nothing`",
+    ),
+)
+check_initial_state(::Nothing, n) = nothing
+function check_initial_state(x::AbstractArray, n)
+    if length(x) != n
+        throw(
+            ArgumentError(
+                "incorrect number of initial states (expected $n, received $(length(x))"
+            ),
+        )
+    end
+
+    return nothing
+end